User: chriad

gravatar for chriad
chriad0
Reputation:
0
Status:
New User
Location:
Last seen:
1 month, 2 weeks ago
Joined:
1 year, 6 months ago
Email:
c***********************@fmi.ch

Posts by chriad

<prev • 6 results • page 1 of 1 • next >
0
votes
2
answers
158
views
2
answers
problems when working with SingleCellExperiment object in scater
... Hi, I have a SingleCellExperiment object: class: SingleCellExperiment dim: 27998 3265 metadata(0): assays(1): counts rownames(27998): ENSMUSG00000051951 ENSMUSG00000089699 ... ENSMUSG00000096730 ENSMUSG00000095742 rowData names(2): id symbol colnames: NULL colData names(2): dataset barcode reduce ...
scater singlecellexperiment written 7 weeks ago by chriad0 • updated 7 weeks ago by davis90
1
vote
1
answer
930
views
1
answer
Plotting several heatmaps onto the same grid with the ComplexHeatmap package in R
... My question is related to this one: http://stackoverflow.com/questions/13081310/combining-multiple-complex-plots-as-panels-in-a-single-figure I also have a unsatisfactory solution based on the answer to the above questions. I'd like a plot like this: I use the following code for this figure: ...
complexheatmap written 14 months ago by chriad0 • updated 14 months ago by jokergoo110
0
votes
0
answers
479
views
0
answers
Error in summarizeOverlaps: Error in names(res) <- nms; 'names' attribute [15] must be the same length as the vector [2]
... Edit: One of my bam files has size 0 on disk! I get the following error when I call summarizeOverlpas:   Error in names(res) <- nms :   'names' attribute [15] must be the same length as the vector [2] Calls: summarizeOverlaps ... .dispatchBamFiles -> bplapply -> bplapply -> bplapply - ...
biocparallel software error summarizeoverlaps written 14 months ago by chriad0
2
votes
1
answer
361
views
1
answer
csaw with negative controls
... Say I'd like to assess 'differential binding' of a histon mark (K9me2) in two conditions (mutant vs wildtype), So I try to answer the question how much binding of the histon mark changes when changing from wlidtype to mutant. I have 2 replicates for each condition, each with a matching input (8 lib ...
csaw written 16 months ago by chriad0
0
votes
1
answers
450
views
1
answers
Comment: C: csaw filterWindows function results in a warning: ("Zero library size detected."
... I use filter=0 in windowCounts, because I had to parallelize and filter!=0 would result in SummarizedExperiment instances with different row counts that couldn't be joined afterwards: WIDTH=10000 se <- mclapply(X=Rsamtools::path(bfl), FUN=windowCounts, param=param.csaw, bin=T, width=WIDTH, filt ...
written 18 months ago by chriad0
1
vote
1
answer
450
views
1
answer
csaw filterWindows function results in a warning: ("Zero library size detected.")
... I have a summarizedExperiment with ChIP and input counts and I'd like to use the filterWindows function.   > s641 class: RangedSummarizedExperiment dim: 10030 2 metadata(48): spacing width ... shift final.ext assays(1): counts rownames: NULL rowData names(1): mappableFractionPerRange colname ...
csaw written 18 months ago by chriad0 • updated 18 months ago by Aaron Lun17k

Latest awards to chriad

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 146 users visited in the last hour